9 The Nucleus

Student Learning Outcomes: Nucleus distinguishes Eukaryotes from Prokaryotes

• Explain general structures of Nuclear Envelope, Nuclear Lamina, Nuclear Pore Complex

• Explain movement of proteins and RNA between Nucleus and Cytoplasm

Selective traffic of proteins, RNAs regulates gene expression

[Describe the Internal Organization of the Nucleus]

• Describe the Nucleolus and rRNA Processing

Nuclear Envelope;Traffic between Nucleus and Cytoplasm

1. Nuclear envelope:• Two membranes• Underlying nuclear lamina• Nuclear pore complexes

• Outer membrane continuous with ER; membrane proteins bind cytoskeleton• Inner membrane proteins bind nuclear

lamina

Fig. 9.1: EM of nucleusarrows indicate nuclear pores

Nuclear membrane, nuclear pores

Each nuclear membrane is phospholipid bilayer permeable only to small nonpolar molecules.

Nuclear pore complexes are sole channels for small polar molecules, ions, proteins, RNA to pass through nuclear envelope.

Fig. 9.1 Outer membrane is continuous with ER;Note ribosomes on ER

Fig. 9.2: EM of nucleusarrows indicate nuclear pores

Nuclear Envelope,Traffic between Nucleus and Cytoplasm

Nuclear lamina is fibrous mesh (structural support):• Fibrous proteins (lamins), and other proteins.• Mutations in lamin genes cause inherited diseases

Hutchinson-Gilford Progeria causes premature aging; Mutations in LMNA gene affect Lamin A protein

Fig. 9.3: EM of nuclear lamina

Nuclear Envelope, Traffic between Nucleus and Cytoplasm

Mammals have 3 lamin genes, (A, B, and C), which code for at least 7 proteins.

Two lamins form dimer, α-helical regions of 2 polypeptide chains wind around each other -> coiled coil.

Lamin dimers associate to form nuclear lamina.

Fig. 9.4

Nuclear Envelope, Traffic between Nucleus and Cytoplasm

Nuclear pore complexes• large 120 nm • Complex: vertebrates, 30 different proteins

(nucleoporins)• Circular structures on faces of membrane;

8-fold symmetry.

Lamina: loose mesh in nucleus Lamins bind: • Protein emerin, lamin B receptor (LBR) (inner membrane) • Chromatin.

. Figs. 9.5, 9,7

Nuclear Pore,Traffic between Nucleus and Cytoplasm

Nuclear pore complex - 8 spokes connected to rings at nuclear and cytoplasmic surfaces.

• Spoke-ring assembly surrounds central channel • Protein filaments extend from rings:• Basketlike structure on nuclear side.• Cytoplasmic filaments on cytoplasmic side

Fig. 9.8 nuclearPore complex

Nuclear Pore Complex, Traffic between Nucleus and Cytoplasm

Nuclear Pore Complex controls traffic betweennucleus and cytoplasm: critical for physiology Passive transport: • small molecules pass freely through channels

Selective transport: energy-dependent • for macromolecules (proteins and RNAs)

Fig. 9.6 nuclear pore complex controls transport

Nuclear Envelope, Traffic between Nucleus and Cytoplasm

A, kinase with SV40 NLS; B, mutated NLS

Nuclear localization signals (NLS):Required for proteins to enter nucleus- specific aa seqRecognized by nuclear transport receptors• transport of proteins through nuclear pore• first identified on SV40 T antigen (viral replication protein)• mutants helped figure

Some NLS are one aa seqOthers bipartitate seq

Nuclear Envelope, Traffic between Nucleus and Cytoplasm

Import of proteins to nucleus:NLS recognized by nuclear transport receptors – importinsActivity of nuclear transport receptors regulated by Ran, a GTP-

binding protein• Importins bind cargo at NLS sequence• Move through pore • Ran-GTP unloads, takes importin out. High concentration of Ran/GTP in nucleus: • enzyme localization:• GAP does GTP hydrolysis in cytoplasm• GEF does GDP/ GTP exchange in nucleus (Fig. 9.20)

Fig. 9.11 import of proteins

Nuclear Envelope, Traffic between Nucleus and Cytoplasm

Nuclear export signals (NES): • Required for proteins targeted for export • Signals recognized by exportins (receptors in nucleus) direct transport to cytoplasm

• Less well characterized than NLS

Ran also required for nuclear export

Ran/GTP promotes binding of exportins and their cargo proteins, Ran/GTP dissociates complexes between

importins and cargos (see Fig. 9.10)

Fig. 9.12 export of proteins

Many importins and exportins are family of nuclear transport receptors - karyopherins.

Nuclear Envelope, Traffic between Nucleus and Cytoplasm

Regulation of Protein transport is another point at which nuclear protein activity can be controlled:

• Regulation of import, export of transcription factors:• Inhibitors block import (IkB and NF-kB) • phosphorylation can block import (de-PO4 releases)

Fig. 9.13 regulated import

Nuclear Envelope, Traffic between Nucleus and Cytoplasm

Most RNAs are exported from nucleus to cytoplasm to function in protein synthesis:

• Active, energy-dependent process requires transport receptors• Transported as ribonucleoprotein complexes (RNPs).

• rRNAs associate with ribosomal proteins, specific RNA processing proteins in nucleolus (Fig. 9.31).

• mRNAs associate with 20 proteins during processing, transport

Fig. 9.14 EM of RNP transport :insect salivary gland; RNA unfolds

Fig 9.15 Transport of snRNAs between nucleus and cytoplasm

Many small RNAs (snRNAs, snoRNAs) function in nucleus.• snRNAs are transported to cytoplasm by exportin (Crm1)• associate with proteins to form snRNPs and return to nucleus;

snRNPs function in splicing

Fig. 9.15 RNA

Internal Organization of the Nucleus

2. Internal structure of nucleus: organized, localized• In animal cells, lamins where chromatin attachmes, organize

other proteins into functional nuclear bodies• Heterochromatin highly condensed, transcriptionally inactive; • Euchromatin decondensed, all overChromosomes organized in territories:• Actively transcribed genes at periphery

Fig. 9.16 arrow = nucleolus; arrowheads = heterochromatinFig. 9.19 mammalian nucleus:DNA probes to chrom 4

Internal Organization of the Nucleus

Nuclear processes appear localized (sequestered) to distinct subnuclear regions:

• DNA replication:• Mammalian cells: clustered sites labeling newly synthesized

DNA with bromodeoxyuridine (BrdU in place of T) • Immunofluorescence (Ab to BrdU):

newly replicated DNA in discrete clusters

Fig. 21 –A: early replicationB, late replication

Internal Organization of the Nucleus

Nuclear processes appear localized (sequestered) to distinct subnuclear regions

• nuclear speckles: mRNA splicing machinery• Detect with immunofluorescent staining - antibodies against snRNPs and splicing factors.• PML bodies have transcription factors, chromatin-modifying proteins; identified from

protein in promyelocytic leukemia

Fig. 9.22SpecklesFig. 9.23 PML bodies

The Nucleolus and rRNA Processing

Fig. 9.26 Xenopus oocyte rRNA genes

*3. Nucleolus: Site of rRNA transcription, processing, some aspects of ribosome assembly.

• Actively growing mammalian cells have 5 to 10 x 106 ribosomes, must be synthesized each time cell divides.

• Nucleolus is not surrounded by a membrane

• Multiple copies of rRNA genes (200 human)• In oocytes, rRNA genes amplified, synthesis for early development.• rRNA genes amplified 2000-fold in Xenopus oocytes, thousands of nucleoli, →1012 ribosomes per oocyte

The Nucleolus and rRNA Processing

Nucleolar organizing regions: • After each cell division, nucleoli reform, associated to genes for 5.8S,

18S, and 28S rRNA genes• Each nucleolar organizing region has tandemly repeated rRNA genes

separated by spacer DNA• 5.8S, 18S, and 28S rRNAs are transcribed as single unit in nucleolus by

RNA pol I → 45S ribosomal precursor RNA

Fig. 9.28

Fig. 9.25

Fig 9.29 Processing of pre-rRNA

Primary transcript of rRNA genes is large 45S pre-rRNA• pre-rRNA processed via series of cleavages, and some base

modifications, including methylations• snoRNPs (snoRNAs with proteins) assemble on pre-rRNA as

processing complexes (like spliceosomes on pre-mRNA)

Fig. 9.29ETS, external transcribedITS, internal transcribed

Fig 9.31 Ribosome assembly

Formation of ribosomes requires assembly of pre-rRNA with ribosomal proteins and 5S rRNA, then export of subunits• pol II made the mRNA for ribosomal proteins.

Fig. 9.31

Review questions:1. Eukaryote nuclear membranes separate transcription from

translation. What regulatory mechanisms unique to eukaryotes achieve this regulation?

3. If you inject a frog egg with two globular proteins, one 15 kd and the other 100 kd, both of which lack NLS, will either protein enter the nucleus?

4. What determines the directionality of nuclear import?

5. Describe how the activity of a transcription factor can be regulated by nuclear import.

* Consider the effect of mutations at gene level that inactivate NLS, NES, prevent phosphorylation of key sites, or prevent binding inhibitors on function